Not Really. May be my view is a bit skewed, since we haven't developed and deployed EJBs in Websphere. But,
Servlets and JSPs and other components of a Web Application posed no problem when developed outside of VAJ and deployed in WebSphere. It wasn't really difficult either. May be using VAJ makes it a lot easier than the normal routine but I wouldn't prefer it for the simple reason that you would be out of touch with the intricacies of this routine.